Captivate doesn't always pick up every single screen event for some software applications. If you were recording audio at the same time, I'm assuming you might have had the camera shutter sound turned off so as not to interfere with your voiceover? If so, you may not have been aware that Cp wasn't actually capturing as many slides as you thought. Try doing a simple test without recording audio with the shutter sound turned up loud enough to hear. Does it show that many captures are being made but only a few survive? Or does it indicate only a few captures are actually taken?

I usually use quite a few manual captures along the way to ensure coverage of all events in the screen.

I change the normal Print Screen button that Captivate sets as default for manual capture to F2 instead because it allows me to make manual captures easily with my left hand while operating the mouse with my right hand. The Print Screen button is far to the right on my keyboard. But F2 is much easier to reach.

After you've realised that Automatic Capture cannot be trusted to get every single screen change, doing manual captures becomes essential.